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Bug: Haplotype Caller Odd VCF files

aeonsimaeonsim Member
edited April 2014 in Ask the GATK team

Hi I've just been having a go with the new Haplotype Caller method and I've getting some odd or malformed lines in the VCF file for example:

For example the format line has declared we should have 4 fields for each Sample record but instead we have samples with 2 records.

Two examples are shown here:

See Block 1
GT:DP:GQ:PL 1/1:.:3:32,3,0 ./.:0

Or where the format block declares 5 fields and we get 3 instead:

GT:AD:DP:GQ:PL  0/0:1,1,0,0,0,0,0,0,0:2:3:0,3,24,3,24,24        ./.:.:0 0/0:1,0,0,0,0,0,0,0,0:1:1:0,1,40,3,41,43        ./.:.:3

Full blocks, Block 1

chr1    3489714 .       G       A       9667.23 .       AC=154;AF=1.00;AN=154;DP=0;FS=0.000;InbreedingCoeff=-0.0391;MLEAC=154;MLEAF=1.00;MQ=0.00;MQ0=0;EFF=INTRAGENIC(MODIFIER|||||TIAM1||CODING|||1),INTRON(MODIFIER||||649|TIAM1|protein_coding|CODING|ENSBTAT00000064124|1|1);CSQ=A|ENSBTAG00000017839|ENSBTAT00000064124|Transcript|intron_variant||||||||1/5||1|TIAM1|HGNC|      GT:DP:GQ:PL     1/1:.:3:32,3,0  1/1:.:18:207,18,0     1/1:.:6:78,6,0  1/1:.:12:140,12,0       1/1:.:9:101,9,0 ./.:0   1/1:.:9:97,9,0  1/1:.:9:96,9,0  1/1:.:21:244,21,0       1/1:.:12:138,12,0       1/1:.:12:124,12,0       1/1:.:9:105,9,0 1/1:.:15:164,15,0     1/1:.:15:153,15,0       1/1:.:27:265,27,0       1/1:.:12:125,12,0       1/1:.:18:214,18,0       ./.:0   1/1:.:9:108,9,0 1/1:.:15:169,15,0       ./.:0   1/1:.:6:76,6,0  1/1:.:6:66,6,0  1/1:.:12:140,12,0     1/1:.:3:28,3,0  1/1:.:3:10,3,0  1/1:.:12:128,12,0       ./.:0   1/1:.:18:181,18,0       1/1:.:9:98,9,0  1/1:.:15:161,15,0       1/1:.:15:185,15,0       1/1:.:12:133,12,0       1/1:.:15:175,15,0     1/1:.:18:178,18,0       1/1:.:12:133,12,0       1/1:.:9:105,9,0 1/1:.:12:141,12,0       1/1:.:15:166,15,0       1/1:.:9:108,9,0 1/1:.:15:160,15,0       1/1:.:27:267,27,0       1/1:.:21:218,21,0    1/1:.:9:107,9,0  1/1:.:3:28,3,0  1/1:.:9:80,9,0  1/1:.:6:46,6,0  ./.:0   1/1:.:6:61,6,0  1/1:.:21:241,21,0       1/1:.:15:161,15,0       1/1:.:6:82,6,0  1/1:.:12:143,12,0       1/1:.:9:109,9,0 1/1:.:21:249,21,0     1/1:.:6:40,6,0  1/1:.:9:94,9,0  1/1:.:15:185,15,0       1/1:.:12:129,12,0       1/1:.:12:132,12,0       ./.:0   1/1:.:21:207,21,0       1/1:.:12:136,12,0       1/1:.:12:109,12,0       1/1:.:18:192,18,0     ./.:0   1/1:.:9:68,9,0  1/1:.:12:138,12,0       1/1:.:6:73,6,0  1/1:.:9:105,9,0 1/1:.:9:98,9,0  1/1:.:6:65,6,0  ./.:0   1/1:.:6:65,6,0  ./.:0   1/1:.:6:58,6,0  1/1:.:12:131,12,0       ./.:0   ./.:01/1:.:3:38,3,0   1/1:.:3:37,3,0  1/1:.:21:227,21,0       1/1:.:12:131,12,0       1/1:.:6:66,6,0  1/1:.:9:100,9,0 1/1:.:21:209,21,0       1/1:.:6:63,6,0  1/1:.:6:69,6,0

Block 2

chr1    55248   .       ACCC    A,CCCC  179.69  .       AC=13,6;AF=0.100,0.046;AN=130;BaseQRankSum=0.736;ClippingRankSum=0.736;DP=347;FS=0.000;InbreedingCoeff=0.2231;MLEAC=10,4;MLEAF=0.077,0.031;MQ=53.55;MQ0=0;MQRankSum=0.736;QD=4.99;ReadPosRankSum=0.736;EFF=INTERGENIC(MODIFIER||||||||||1),INTERGENIC(MODIFIER||||||||||2);CSQ=-||||intergenic_variant|||||||||||||     GT:AD:DP:GQ:PL  0/0:1,1,0,0,0,0,0,0,0:2:3:0,3,24,3,24,24        ./.:.:0 0/0:1,0,0,0,0,0,0,0,0:1:1:0,1,40,3,41,43        0/0:1,0,0,0,0,0,0,0,0:1:2:0,2,44,3,45,46        0/0:.:5:0:0,0,103,0,103,103     0/0:3,0,1,0,0,0,0,0,0:4:9:0,9,81,9,81,81        0/0:0,0,1,0,0,0,0,0,0:1:1:0,1,2,1,2,2   ./.:.:1 0/0:.:3:0:0,0,41,0,41,41        0/0:1,0,0,0,0,0,0,0,0:1:9:0,9,73,9,73,73        0/1:1,0,0,1,0,0,0,0,0:2:22:28,0,73,28,22,46     0/0:1,0,0,0,0,0,0,0,0:1:4:0,4,25,4,25,25        0/0:2,0,0,0,0,0,0,0,0:2:21:0,21,273,21,273,273  0/1:5,0,0,1,0,0,0,0,0:6:11:11,0,235,26,158,175  ./.:0,0,0,0,1,0,0,0,0:1 0/0:.:4:0:0,0,46,0,46,46        ./.:.:3 ./.:.:2 0/1:1,0,1,1,0,0,0,0,0:3:21:28,0,44,31,21,52     0/0:.:4:0:0,0,77,0,77,77        0/0:0,0,1,0,0,0,0,0,0:1:1:0,1,2,1,2,2   0/0:.:2:6:0,6,51,6,51,51        0/0:.:6:2:0,2,151,2,151,151     0/0:2,0,1,0,0,0,0,0,0:3:7:0,7,74,7,74,74        ./.:.:0 0/0:2,0,0,0,0,0,0,0,0:2:5:0,7,59,5,37,35        1/2:0,0,0,1,0,0,0,0,0:1:1:27,1,40,26,0,25       0/0:2,0,0,0,0,0,0,0,0:2:9:0,9,83,9,83,83        ./.:.:0 2/2:0,0,0,0,0,3,0,0,0:3:9:59,59,59,9,9,0        ./.:.:16        0/0:2,0,0,0,0,0,0,0,0:2:7:0,7,59,7,59,59        0/0:2,0,0,0,0,0,0,0,0:2:9:0,9,83,9,83,83        0/0:2,0,0,0,0,0,0,0,0:2:11:0,11,68,11,68,68     0/2:6,0,0,0,0,2,0,0,0:8:18:18,39,384,0,346,340  ./.:.:1 0/1:3,0,0,1,0,0,0,0,0:4:25:25,0,96,34,100,134   0/0:2,0,0,0,0,0,0,0,0:2:12:0,12,105,12,105,105  0/1:1,0,0,1,0,0,0,0,0:2:17:17,0,94,21,26,44     0/0:.:2:6:0,6,64,6,64,64        0/0:1,0,0,0,0,0,0,0,0:1:2:0,2,24,3,25,27        0/0:.:2:6:0,6,48,6,48,48        0/0:.:2:6:0,6,63,6,63,63        0/0:0,0,1,0,0,0,0,0,0:1:0:0,0,1,0,1,1   ./.:.:0 0/0:1,0,0,0,0,0,0,0,0:1:1:0,1,6,3,8,9   0/0:1,0,0,0,0,0,0,0,0:1:15:0,15,124,15,124,124  ./.:.:0 0/0:1,0,0,0,0,0,0,0,0:1:4:0,4,19,4,19,19        0/1:2,0,0,1,0,0,0,0,0:3:28:28,0,66,34,70,104    0/0:.:4:0:0,0,18,0,18,18        0/2:2,0,0,0,0,4,0,0,0:6:57:68,74,143,0,69,57    ./.:.:0 0/0:4,0,0,0,0,0,0,0,1:5:15:0,15,109,15,109,109  0/0:.:10:0:0,0,182,0,182,182    0/0:.:1:3:0,3,31,3,31,31        0/0:0,0,1,0,0,0,0,0,0:1:1:0,1,2,1,2,2   0/0:2,0,0,0,0,0,0,0,0:2:5:0,5,76,6,78,79        0/0:1,1,0,0,0,0,0,0,0:2:4:0,4,28,4,28,28        ./.:.:1 1/1:0,0,0,2,0,0,0,0,0:2:6:67,6,0,67,6,67        ./.:.:1 0/0:.:2:0:0,0,14,0,14,14        ./.:.:0 ./.:.:1 0/0:.:5:1:0,1,120,1,120,120     0/0:.:4:0:0,0,8,0,8,8   0/0:.:6:0:0,0,94,0,94,94        0/1:1,0,0,2,0,0,0,0,0:3:1:27,0,1,29,6,35        0/0:.:2:0:0,0,3,0,3,3   ./.:.:6 ./.:.:0 ./.:.:0 0/2:3,0,0,0,0,2,0,0,0:5:27:46,27,89,0,62,81     ./.:.:0 0/0:.:1:0:0,0,6,0,6,6   0/0:.:9:0:0,0,86,0,86,86        ./.:.:1 ./.:.:0 1/1:.:.:0:1,1,0,1,0,0   0/0:0,0,0,0,0,0,0,0,0:0:3:0,3,26,3,26,26        0/1:4,0,0,2,0,0,0,0,0:6:49:49,0,93,61,100,160   0/0:.:3:0:0,0,14,0,14,14        0/0:.:8:0:0,0,60,0,60,60        0/0:2,1,0,0,0,0,0,0,0:3:6:0,6,37,6,37,37        ./.:.:2 0/0:.:9:0:0,0,81,0,81,81        0/0:0,0,0,0,0,0,0,0,0:0:1:0,1,2,1,2,2

Any idea what the issue is?

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